Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Towards recombinantly produced milk proteins : Physicochemical and emulsifying properties of engineered whey protein beta-lactoglobulin variants
    Keppler, Julia K. ; Heyse, Anja ; Scheidler, Eva ; Uttinger, Maximilian J. ; Fitzner, Laura ; Jandt, Uwe ; Heyn, Timon R. ; Lautenbach, Vanessa ; Loch, Joanna I. ; Lohr, Jonas ; Kieserling, Helena ; Günther, Gabriele ; Kempf, Elena ; Grosch, Jan Hendrik ; Lewiński, Krzysztof ; Jahn, Dieter ; Lübbert, Christian ; Peukert, Wolfgang ; Kulozik, Ulrich ; Drusch, Stephan ; Krull, Rainer ; Schwarz, Karin ; Biedendieck, Rebekka - \ 2021
    Food Hydrocolloids 110 (2021). - ISSN 0268-005X
    Two recombinant beta-lactoglobulin (BLG) B variants were produced in E. coli. Production/isolation resulted in native BLG without post-translational modifications. Properties of recombinant variants were compared to commercial BLG B and BLG AB. Minor differences in solubility and interface adsorption behavior were evident. Genetically engineered and natural BLGs show similar emulsifying properties.
    Erratum: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020)1. - ISSN 2399-3642 - 1 p.


    Progettazione urbana bioclimatica. Obiettivi e metodi
    Cortesão, J. - \ 2020
    In: Nuove sfide per l’architettura del paesaggio contemporanea Un ritorno verso la natura? / Burlando, Patrizia, Cortesão, João, Mazzino, Francesca, Piel, Christian, Florence : Altralinea Edizioni - ISBN 9788894869910 - p. 40 - 49.
    Bioclimatic urban design is a perspective on urban design fuelled by the belief that it is possible to mitigate urban climate problems through design and, thereby, actively contribute to a better mediation between man and climate. Bioclimatic urban design expands the scope of common urban design with the inclusion of design measures targeted at climate-resilience. This leads to including specific methods and tools, and looking at common urban design elements through a different lens. This book chapter presents an overview on what bioclimatic urban design is, on its fundamental goals and methods.
    Feature-based molecular networking in the GNPS analysis environment
    Nothias, Louis Félix ; Petras, Daniel ; Schmid, Robin ; Dührkop, Kai ; Rainer, Johannes ; Sarvepalli, Abinesh ; Protsyuk, Ivan ; Ernst, Madeleine ; Tsugawa, Hiroshi ; Fleischauer, Markus ; Aicheler, Fabian ; Aksenov, Alexander A. ; Alka, Oliver ; Allard, Pierre Marie ; Barsch, Aiko ; Cachet, Xavier ; Caraballo-Rodriguez, Andres Mauricio ; Silva, Ricardo R. Da; Dang, Tam ; Garg, Neha ; Gauglitz, Julia M. ; Gurevich, Alexey ; Isaac, Giorgis ; Jarmusch, Alan K. ; Kameník, Zdeněk ; Kang, Kyo Bin ; Kessler, Nikolas ; Koester, Irina ; Korf, Ansgar ; Gouellec, Audrey Le; Ludwig, Marcus ; Martin H, Christian ; McCall, Laura Isobel ; McSayles, Jonathan ; Meyer, Sven W. ; Mohimani, Hosein ; Morsy, Mustafa ; Moyne, Oriane ; Neumann, Steffen ; Neuweger, Heiko ; Nguyen, Ngoc Hung ; Nothias-Esposito, Melissa ; Paolini, Julien ; Phelan, Vanessa V. ; Pluskal, Tomáš ; Quinn, Robert A. ; Rogers, Simon ; Shrestha, Bindesh ; Tripathi, Anupriya ; Hooft, Justin J.J. van der; Vargas, Fernando ; Weldon, Kelly C. ; Witting, Michael ; Yang, Heejung ; Zhang, Zheng ; Zubeil, Florian ; Kohlbacher, Oliver ; Böcker, Sebastian ; Alexandrov, Theodore ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
    Nature Methods : techniques for life scientists and chemists 17 (2020)9. - ISSN 1548-7091 - p. 905 - 908.

    Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.

    COLOSS survey: global impact of COVID-19 on bee research
    Dall’Olio, Raffaele ; Blacquiere, Tjeerd ; Bouga, Maria ; Brodschneider, Robert ; Carreck, Norman L. ; Chantawannakul, Panuwan ; Dietemann, Vincent ; Kristiansen, Lotta Fabricius ; Gajda, Anna ; Gregorc, Ales ; Ozkirim, Aslı ; Pirk, Christian ; Soroker, Victoria ; Williams, Geoffrey R. ; Neumann, Peter - \ 2020
    Journal of Apicultural Research (2020). - ISSN 0021-8839
    Apis mellifera - COLOSS - coronavirus - COVID-19 - extension - honey bee - pandemic - research

    The socio-economic impacts of COVID-19 on society have yet to be truly revealed; there is no doubt that the pandemic has severely affected the daily lives of most of humanity. It is to be expected that the research activities of scientists could be impacted to varying degrees, but no data exist on how COVID-19 has affected research specifically. Here, we show that the still ongoing COVID-19 pandemic has already diversely and negatively affected bee research at a global level. An online survey disseminated through the global COLOSS honey bee research association showed that every participant (n = 230 from 56 countries) reported an impact on one or more of their activities. Activities that require travelling or the physical presence of people (meetings and conferences, teaching and extension) were affected the most, but also laboratory and field activities, daily operations, supervision and other activities were affected to varying degrees. Since the basic activities are very similar for many research fields, it appears as if our findings for bee research can be extrapolated to other fields. In the light of our data, we recommend that stakeholders such as governments and funding bodies who support research should facilitate the wide implementation of web-based information technology required for efficient online communication for research and education, as well as adequately loosened restriction measures with respect to field and laboratory work. Finally, increased flexibility in administration and extension of research grants and fellowships seem to be needed. It is apparent that adequate responses by all stakeholders are required to limit the impact of COVID-19 and future pandemics on bee science and other research fields.

    Analyzing the economics of food loss and waste reductions in a food supply chain
    Gorter, Harry de; Drabik, Dušan ; Just, David R. ; Reynolds, Christian ; Sethi, Geeta - \ 2020
    Food Policy (2020). - ISSN 0306-9192
    Cascading effects - Effective prices - Food waste - Purchases vs. sales - Supply chain

    The paper provides an economic model of food waste for consumers, intermediaries and farmers based on first principles. We distinguish between purchases and sales for each intermediary, purchases and consumption for consumers, and gross production versus sales for farmers. Because of waste at each stage of the supply chain, agents need higher sales prices to compensate. Our model is able to make more accurate predictions of how interventions (public policies or private initiatives) designed to reduce food waste influence the markets overall, including indirect (cascading) effects. We show the uniqueness of these interaction effects with a formal model and simulate an empirical model calibrated to market parameters and rates of waste for two commodities (chicken and fruit) in the UK. We show that the impacts of reducing waste vary by commodity, depending on supply and demand elasticities, degree of openness to international trade and the initial rates of food loss and waste at each stage of the value chain. The cascading effects up and down the supply chain mean that in some cases interventions to reduce food waste will be reinforced while in other cases partially offset.

    Lake trout growth is sensitive to spring temperature in southwest Alaska lakes
    Biela, Vanessa R. von; Black, Bryan A. ; Young, Daniel B. ; Sleen, Peter van der; Bartz, Krista K. ; Zimmerman, Christian E. - \ 2020
    Ecology of Freshwater Fish (2020). - ISSN 0906-6691
    biochronology - growth - lake trout - marine-derived nutrients - Pacific salmon - temperature

    In high-latitude lakes, air temperature is an important driver of ice cover thickness and duration, which in turn influence water temperature and primary production supporting lake consumers and predators. In lieu of multidecadal observational records necessary to assess the response of lakes to long-term warming, we used otolith-based growth records from a long-lived resident lake fish, lake trout (Salvelinus namaycush), as a proxy for production. Lake trout were collected from seven deep, oligotrophic lakes in Lake Clark National Park and Preserve on in southwest Alaska that varied in the presence of marine-derived nutrients (MDN) from anadromous sockeye salmon (Oncorhynchus nerka). Linear mixed-effects models were used to partition variation in lake trout growth by age and calendar-year and model comparisons tested for a mean increase in lake trout growth with sockeye salmon presence. Year effects from the best mixed-effects model were subsequently compared to indices of temperature, lake ice, and regional indices of sockeye salmon escapement. A strong positive correlation between annual lake trout growth and temperature suggested that warmer springs, earlier lake ice break-up, and a longer ice-free growing season increase lake trout growth via previously identified bottom-up increases in production with warming. Accounting for differences in the presence or annual escapement of sockeye salmon with available data did not improve model fit. Collectively with other studies, the results suggest that productivity of subarctic lakes has benefitted from warming spring temperatures and that temperature can synchronise otolith growth across lakes with and without sockeye salmon MDN.

    Next-generation biological control: the need for integrating genetics and genomics
    Leung, Kelley ; Ras, Erica ; Ferguson, Kim B. ; Ariëns, Simone ; Babendreier, Dirk ; Bijma, Piter ; Bourtzis, Kostas ; Brodeur, Jacques ; Bruins, Margreet A. ; Centurión, Alejandra ; Chattington, Sophie R. ; Chinchilla-Ramírez, Milena ; Dicke, Marcel ; Fatouros, Nina E. ; González-Cabrera, Joel ; Groot, Thomas V.M. ; Haye, Tim ; Knapp, Markus ; Koskinioti, Panagiota ; Hesran, Sophie Le; Lyrakis, Manolis ; Paspati, Angeliki ; Pérez-Hedo, Meritxell ; Plouvier, Wouter N. ; Schlötterer, Christian ; Stahl, Judith M. ; Thiel, Andra ; Urbaneja, Alberto ; Zande, Louis van de; Verhulst, Eveline C. ; Vet, Louise E.M. ; Visser, Sander ; Werren, John H. ; Xia, Shuwen ; Zwaan, Bas J. ; Magalhães, Sara ; Beukeboom, Leo W. ; Pannebakker, Bart A. - \ 2020
    Biological Reviews (2020). - ISSN 1464-7931
    artificial selection - biological control - genetics - genome assembly - genomics - insect breeding - microbiome - modelling

    Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

    Swimming alone? Why linking flood risk perception and behavior requires more than “it's the individual, stupid”
    Rufat, Samuel ; Fekete, Alexander ; Armaş, Iuliana ; Hartmann, Thomas ; Kuhlicke, Christian ; Prior, Tim ; Thaler, Thomas ; Wisner, Ben - \ 2020
    Wiley Interdisciplinary Reviews: Water 7 (2020)5. - ISSN 2049-1948
    behavior - disaster risk reduction - flood - flood risk management - risk perception

    A common assertion in discussions of flooding is that risk perception is critical and is linked to risk-mitigating behavior. Furthermore, many assert that the adverse effects of floods could be reduced by changes in risk communication, thereby influencing risk perception to foster mitigating behavior. We argue that these assertions are based on quite questionable underlying assumptions: That stakeholders are generally aware of flood risk, that they have the capacity to engage in disaster risk reduction, and that their actions can be effective. The belief in and policies influenced by these three questionable assertions support, in turn, policies that shift responsibility for flood risk reduction onto individuals and homeowners, without regard for social and spatial justice issues. In contrast, we argue that context matters to understanding the complexity of the relation between flood risk perception and behavior, local power relations, and other constraints and opportunities that affect stakeholders. While the academic community has long played a pivotal role in supporting practical flood risk management, future research should take a more critical perspective on the underlying assumptions and focus on improving coordination across theories, methods, and variables, fostering comparative studies across disciplines, contexts, and scales. This article is categorized under: Engineering Water > Planning Water Human Water > Water as Imagined and Represented Science of Water > Water Extremes.

    A Biostimulant Seed Treatment Improved Heat Stress Tolerance During Cucumber Seed Germination by Acting on the Antioxidant System and Glyoxylate Cycle
    Campobenedetto, Cristina ; Grange, Eric ; Mannino, Giuseppe ; Arkel, Jeroen van; Beekwilder, Jules ; Karlova, Rumyana ; Garabello, Christian ; Contartese, Valeria ; Bertea, Cinzia M. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    antioxidant molecules and enzymes - biostimulant - Cucumis sativus - gene expression - isocitrate lyase - seed treatment

    Seed enhancement technologies have the potential to improve germination and seedling growth under environmental stress. The effects of KIEM®, an innovative biostimulant based on lignin derivatives and containing plant-derived amino acids and molybdenum, were investigated on cucumber (Cucumis sativus L.) seed germination. To determine the metabolic targets of this product, biometric, transcriptional and biochemical analyses were carried out on both non-treated and KIEM®-treated seeds incubated for 24 and 48 h under standard (28°C) and heat stress (35°C) conditions. The application of the biostimulant as a seed treatment increased the percent germination (+6.54%) and fresh biomass (+13%) at 48 h, and decreased the content of H2O2 in treated seeds at 28°C (−70%) and at 35°C (−80%). These changes in biometric and biochemical properties were accompanied by changes in expression levels of the genes coding for ROS-producing (RBOH) and scavenging (SOD, CAT, GST) enzymes and their specific activity. In general, the treatment with KIEM® in heat-stress condition appeared to stimulate a higher accumulation of three scavenger gene transcripts: CuZnSOD (+1.78), MnSOD (+1.75), and CAT (+3.39), while the FeSOD isoform was dramatically downregulated (0.24). Moreover, the amount of non-protein thiols, important antioxidant molecules, was increased by the biostimulant after 48 h (+20%). Taken together these results suggest that KIEM® acts through mitigation of the effects of the oxidative stress. Moreover, after 48 h, the pre-sowing treatment with KIEM® increased the transcription levels (+1.5) and the activity of isocitrate lyase (+37%), a key enzyme of the glyoxylate cycle, suggesting a potential effect of this product in speeding up the germination process. Finally, the chemical characterization of KIEM® identified five essential and three non-essential amino acids, and others bioactive compounds, including five organic and inorganic acids that might be potentially involved in its activity. Based on these data, insights on the potential mechanism of action of the biostimulant, suggested that there are broader applications as a product able to increase seed tolerance to different abiotic stress typical of adverse environmental conditions.

    Calculation of ventilation rates and ammonia emissions : Comparison of sampling strategies for a naturally ventilated dairy barn
    Janke, David ; Willink, Dylia ; Ammon, Christian ; Hempel, Sabrina ; Schrade, Sabine ; Demeyer, Peter ; Hartung, Eberhard ; Amon, Barbara ; Ogink, Nico ; Amon, Thomas - \ 2020
    Biosystems Engineering 198 (2020). - ISSN 1537-5110 - p. 15 - 30.
    Air exchange rate - CO balance method - FTIR - Long-term measurements - Sampling positions

    Emissions and ventilation rates (VRs) in naturally ventilated dairy barns (NVDBs) are usually measured using indirect methods, where the choice of inside and outside sampling locations (i.e. sampling strategy) is crucial. The goal of this study was to quantify the influence of the sampling strategy on the estimation of emissions and VRs. We equipped a NVDB in northern Germany with an extensive measuring setup capable of measuring emissions under all wind conditions. Ammonia (NH3) and carbon dioxide (CO2) concentrations were measured with two Fourier-transform infrared spectrometers. Hourly values for ventilation rates and emissions for ammonia over a period of nearly a year were derived using the CO2 balance method and five different sampling strategies for the acquisition of indoor and outdoor concentrations were applied. When comparing the strategy estimating the highest emission level to the strategy estimating the lowest, the differences in NH3 emissions in winter, transition, and summer season were +26%, +19% and +11%, respectively. For the ventilation rates, the differences were +80%, +94%, and 63% for the winter, transition and summer season, respectively. By accommodating inside/outside concentration measurements around the entire perimeter of the barn instead of a reduced part of the perimeter (aligned to a presumed main wind direction), the amount of available data substantially increased for around 210% for the same monitoring period.

    Beneficial health effects of chitin and chitosan
    Dong, Liyou ; Wichers, H.J. ; Govers, C.C.F.M. - \ 2020
    In: Chitin and Chitosan / van den Broek, Lambertus A.M., Boeriu, Carmen G., Stevens, Christian V., John Wiley and Sons (Wiley Series in Renewable Research ) - ISBN 9781119450436 - p. 145 - 164.
    Chitin and chitosan have been recognised for their beneficial health effects since the 1980s. Over the past few decades, numerous studies and several clinical trials have been performed which demonstrated that these compounds can reduce body weight and cardiovascular disease (CVD), improve wound healing, but can also modulate the immune system and demonstrate antifungal and antibacterial activity. In particular, weight reduction and improvement of cardiovascular status are interesting targets as the prevalence of obesity and CVD are increasing. Both diseases are associated with various pathological disorders, including diabetes and hypertension and put a strain on healthcare costs and capacity. In general, lifestyle‐based interventions such as the oral intake of chitin and/or chitosan are becoming increasingly popular as these are easily integrated into current treatments and improve the self‐assertiveness of patients. Of interest, but beyond the scope of this chapter, is the use of chitin‐glucans as supplements in cosmetics. Several studies have demonstrated that chitin‐glucan reduced wrinkling and skin‐ageing, suggesting an interaction between the chitin‐glucan and cells of the epidermis. Although these effects may not be attributed to chitin alone, this does demonstrate the strong biological potential of chitin on cells of the human body. In this chapter, scientific literature has been reviewed that demonstrated the beneficial health effects of chitin and chitosan from an immunomodulatory point‐of‐view. First, we provide an overview of in vitro studies that offer in‐depth mechanistic insights, followed by describing preclinical animal studies. Finally, we list various human intervention trials that most clearly demonstrate the beneficial health effects of chitin and chitosan. Furthermore, we purposely discriminate between data on chitin and chitosan as they are chemically distinct and therefore possibly demonstrate unique effects on health
    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography 29 (2020)9. - ISSN 1466-822X - p. 1495 - 1514.
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    Functional relationship of particulate matter (PM) emissions, animal species, and moisture content during manure application
    Kabelitz, Tina ; Ammon, Christian ; Funk, Roger ; Münch, Steffen ; Biniasch, Oliver ; Nübel, Ulrich ; Thiel, Nadine ; Rösler, Uwe ; Siller, Paul ; Amon, Barbara ; Aarnink, André J.A. ; Amon, Thomas - \ 2020
    Environment International 143 (2020). - ISSN 0160-4120 - 12 p.
    Dry matter content - Fine dust - Manure management - Microorganism - Pig - Poultry

    Livestock manure is recycled to agricultural land as organic fertilizer. Due to the extensive usage of antibiotics in conventional animal farming, antibiotic-resistant bacteria are highly prevalent in feces and manure. The spread of wind-driven particulate matter (PM) with potentially associated harmful bacteria through manure application may pose a threat to environmental and human health. We studied whether PM was aerosolized during the application of solid and dried livestock manure and the functional relationship between PM release, manure dry matter content (DM), treatment and animal species. In parallel, manure and resulting PM were investigated for the survival of pathogenic and antibiotic-resistant bacterial species. The results showed that from manure with a higher DM smaller particles were generated and more PM was emitted. A positive correlation between manure DM and PM aerosolization rate was observed. There was a species-dependent critical dryness level (poultry: 60% DM, pig: 80% DM) where manure began to release PM into the environment. The maximum PM emission potentials were 1 and 3 kg t−1 of applied poultry and pig manure, respectively. Dried manure and resulting PM contained strongly reduced amounts of investigated pathogenic and antibiotic-resistant microorganisms compared to fresh samples. An optimal manure DM regarding low PM emissions and reduced pathogen viability was defined from our results, which was 55–70% DM for poultry manure and 75–85% DM for pig manure. The novel findings of this study increase our detailed understanding and basic knowledge on manure PM emissions and enable optimization of manure management, aiming a manure DM that reduces PM emissions and pathogenic release into the environment.

    Natuur als algoritme. Een dag met dieren in een datalandschap
    Driessen, C.P.G. ; Ernsten, Christian - \ 2020
    In: Voorland Groningen: Wandelingen door het Anthropoceen. / Visser, D.J., Ernsten, C., Minkema, M., Rotterdam : Nai 010 Uitgevers/Publishers - ISBN 9789462085909 - p. 150 - 159.
    The ovipositor actuation mechanism of a parasitic wasp and its functional implications
    Meer, Noraly M.M.E. van; Cerkvenik, Uroš ; Schlepütz, Christian M. ; Leeuwen, Johan L. van; Gussekloo, Sander W.S. - \ 2020
    Journal of Anatomy (2020). - ISSN 0021-8782
    hymenoptera - kinematics - musculature - ovipositor - synchrotron X-ray micro-computed tomography

    Parasitic wasps use specialized needle-like structures, ovipositors, to drill into substrates to reach hidden hosts. The external ovipositor (terebra) consists of three interconnected, sliding elements (valvulae), which are moved reciprocally during insertion. This presumably reduces the required pushing force on the terebra and limits the risk of damage whilst probing. Although this is an important mechanism, it is still not completely understood how the actuation of the valvulae is achieved, and it has only been studied with the ovipositor in rest position. Additionally, very little is known about the magnitude of the forces generated during probing. We used synchrotron X-ray microtomography to reconstruct the actuation mechanism of the parasitic wasp Diachasmimorpha longicaudata (Braconidae) in four distinct phases of the probing cycle. We show that only the paired first valvulae of the terebra move independently, while the second valvula moves with the metasoma (‘abdomen’). The first valvula movements are initiated by rotation of one chitin plate (first valvifer) with respect to another such plate (second valvifer). This is achieved indirectly by muscles connecting the non-rotating second valvifer and the abdominal ninth tergite. Contrary to previous reports, we found muscle fibres running inside the terebra, although their function remains unclear. The estimated maximal forces that can be exerted by the first valvulae are small (protraction 1.19 mN and retraction 0.874 mN), which reduces the risk of buckling, but are sufficient for successful probing. The small net forces of the valvulae on the substrate may still lead to buckling of the terebra; we show that the sheaths surrounding the valvulae prevent this by effectively increasing the diameter and second moment of area of the terebra. Our findings improve the comprehension of hymenopteran probing mechanisms, the function of the associated muscles, and the forces and damage-limiting mechanism that are involved in drilling a slender terebra into a substrate.

    The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
    Kallscheuer, Nicolai ; Jeske, Olga ; Sandargo, Birthe ; Boedeker, Christian ; Wiegand, Sandra ; Bartling, Pascal ; Jogler, Mareike ; Rohde, Manfred ; Petersen, Jörn ; Medema, Marnix H. ; Surup, Frank ; Jogler, Christian - \ 2020
    Communications Biology 3 (2020)1. - ISSN 2399-3642

    Bacterial strains of the phylum Planctomycetes occur ubiquitously, but are often found on surfaces of aquatic phototrophs, e.g. alga. Despite slower growth, planctomycetes are not outcompeted by faster-growing bacteria in biofilms on such surfaces; however, strategies allowing them to compensate for slower growth have not yet been investigated. Here, we identified stieleriacines, a class of N-acylated tyrosines produced by the novel planctomycete Stieleria maiorica Mal15T, and analysed their effects on growth of the producing strain and bacterial species likely co-occurring with strain Mal15T. Stieleriacines reduced the lag phase of Mal15T and either stimulated or inhibited biofilm formation of two bacterial competitors, indicating that Mal15T employs stieleriacines to specifically alter microbial biofilm composition. The genetic organisation of the putative stieleriacine biosynthetic cluster in strain Mal15T points towards a functional link of stieleriacine biosynthesis to exopolysaccharide-associated protein sorting and biofilm formation.

    Strategy in complexity: the shaping of communities and environments
    Assche, Kristof van; Beunen, R. ; Duineveld, M. - \ 2020
    In: Handbook on Planning and Complexity / de Roo, Gert, Yamu, Claudia, Zuidema, Christian, Edward Elgar (Research Handbooks in Planning series ) - ISBN 9781786439178 - p. 151 - 170.
    In this chapter, we reflect on the possibilities of purposeful community development in a non-linear understanding of society. Although the complexity and uncertainty that characterize the world put forward challenges for planning and steering, it doesn’t imply that purposive interventions are unlikely to be successful or that planning has become obsolete. It does, however, require a different understanding of how societies organize themselves and about how collective strategies sort reality-effects. Planning, as spatial planning, is a subset of strategy and provides a set of tools for others. In this chapter we highlight the importance of strategy in a world where many of the traditional planning rules and certainties have been challenged. We deepen the discussion about community development by placing it in the context of governance understood as a set of co-evolving actors, institutions, and power/knowledge configurations. Within these ever changing governance systems, forms of organization are necessarily linked to and co-evolve with narratives on identity, community, and governance itself, as the taking of collectively binding decisions. Taking into account the complexity and non-linearity that characterizes these co-evolutionary processes we discuss the links between community formation and the organization and transformation of space through planning. We explore how strategy should be understood in this context and we identify which forms of strategy can work under the structural conditions revealed through the lens of complexity theory and governance theory.
    Hepatocytic c-Jun N-terminal kinases (JNK)-1/2 function determines cell fate during carcinogenesis
    Cubero, Francisco Javier ; Mohamed, Mohamed Ramadan ; Woitok, Marius M. ; Zhao, Gang ; Hatting, Maximilian ; Nevzorova, Yulia A. ; Chen, Chaobo ; Haybaeck, Johannes ; Bruin, Alain de; Avila, Matias A. ; Boekschoten, Mark ; Davis, Roger J. ; Trautwein, Christian - \ 2020
    Wageningen University
    GSE140498 - PRJNA589901 - Mus musculus
    Aberrant biliary hyperproliferation resulting from lack of differentiating signals favoring the maintenance of an immature and proliferative phenotype by biliary epithelial cells are ultimately responsible for ducto/cystogenesis and intrahepatic cholangiocarcinoma (CCA) formation. Mitogen-activated protein kinase (MAPK) signaling is pivotal for CCA-related tumorigenesis. In particular, targeted inhibition of JNK signaling has shown therapeutic potential. However, the cell-type specific role and mechanisms triggered by JNK in liver parenchymal cells during CCA remains largely unknown. Here, we aimed to investigate the relevance of JNK function in hepatocytes in experimental carcinogenesis. JNK signaling in hepatocytes was inhibited by crossing AlbCre-JNK1LoxP/LoxP mice with JNK2-deficient mice to generate Jnk1LoxP/LoxP/Jnk2−/− (JNKΔhepa) mice. JNKΔhepa mice were further interbred with hepatocyte-specific Nemo-knockout mice (NEMOΔhepa), a model of chronic liver inflammation and spontaneous hepatocarcinogenesis, to generate NEMO/JNKΔhepa mice. The impact of JNK deletion on liver damage, cell death, compensatory proliferation, fibrogenesis, and tumor development in NEMOΔhepa mice was determined. Moreover, regulation of essential genes was assessed by RT-PCR, immunoblottings and immunostains. Additionally, JNK2 inhibition, specifically in hepatocytes of NEMOΔhepa/JNK1Δhepa mice, was performed using siRNA (siJnk2) nanodelivery. Finally, active signaling pathways were blocked using specific inhibitors. Compound deletion of JNK1 and JNK2 in hepatocytes diminished hepatocarcinogenesis in both the DEN model of hepatocarcinogenesis and in NEMOΔhepa mice, but, in contrast, caused massive proliferation of the biliary ducts. Indeed, JNK deficiency in hepatocytes of NEMOΔhepa (NEMOΔhepa/JNKΔhepa) animals caused elevated fibrosis, increased apoptosis, increased compensatory proliferation, and elevated inflammatory cytokines expression, but reduced hepatocarcinogenesis. Furthermore, siJnk2 treatment in NEMOΔhepa/JNK1Δhepa mice recapitulated the phenotype of NEMOΔhepa/JNKΔhepa mice. Next, we sought to investigate the impact of molecular pathways in response to compound JNK deficiency in NEMOΔhepa mice. We found that NEMOΔhepa/JNKΔhepa livers exhibited overexpression of the IL-6/Stat3 pathway in addition to EGFR-Raf-MEK-ERK cascade. The functional relevance was tested by administering lapatinib - a dual tyrosine kinase inhibitor (TKI) of ErbB2 and EGFR signaling - to NEMOΔhepa/JNKΔhepa mice. Lapatinib effectively inhibited cystogenesis, improved transaminases and effectively blocked EGFR-Raf-MEK-ERK signaling. Our study defines a novel function of JNK in cell fate as well as hepatocarcinogenesis and opens new therapeutic avenues devised to inhibit pathways of cholangiocarcinogenesis.
    Loss of c‐Jun N‐terminal Kinase 1 and 2 Function in Liver Epithelial Cells Triggers Biliary Hyperproliferation Resembling Cholangiocarcinoma
    Cubero, Francisco Javier ; Mohamed, Mohamed Ramadan ; Woitok, Marius M. ; Zhao, Gang ; Hatting, Maximilian ; Nevzorova, Yulia A. ; Chen, Chaobo ; Haybaeck, Johannes ; Bruin, Alain de; Avila, Matias A. ; Boekschoten, Mark V. ; Davis, Roger J. ; Trautwein, Christian - \ 2020
    Hepatology Communications 4 (2020)6. - ISSN 2471-254X - p. 834 - 851.
    Targeted inhibition of the c‐Jun N‐terminal kinases (JNKs) has shown therapeutic potential in intrahepatic cholangiocarcinoma (CCA)‐related tumorigenesis. However, the cell‐type‐specific role and mechanisms triggered by JNK in liver parenchymal cells during CCA remain largely unknown. Here, we aimed to investigate the relevance of JNK1 and JNK2 function in hepatocytes in two different models of experimental carcinogenesis, the dethylnitrosamine (DEN) model and in nuclear factor kappa B essential modulator (NEMO)hepatocyte‐specific knockout (Δhepa) mice, focusing on liver damage, cell death, compensatory proliferation, fibrogenesis, and tumor development. Moreover, regulation of essential genes was assessed by reverse transcription polymerase chain reaction, immunoblottings, and immunostainings. Additionally, specific Jnk2 inhibition in hepatocytes of NEMOΔhepa/JNK1Δhepa mice was performed using small interfering (si) RNA (siJnk2 ) nanodelivery. Finally, active signaling pathways were blocked using specific inhibitors. Compound deletion of Jnk1 and Jnk2 in hepatocytes diminished hepatocellular carcinoma (HCC) in both the DEN model and in NEMOΔhepa mice but in contrast caused massive proliferation of the biliary ducts. Indeed, Jnk1/2 deficiency in hepatocytes of NEMOΔhepa (NEMOΔhepa/JNKΔhepa) animals caused elevated fibrosis, increased apoptosis, increased compensatory proliferation, and elevated inflammatory cytokines expression but reduced HCC. Furthermore, siJnk2 treatment in NEMOΔhepa/JNK1Δhepa mice recapitulated the phenotype of NEMOΔhepa/JNKΔhepa mice. Next, we sought to investigate the impact of molecular pathways in response to compound JNK deficiency in NEMOΔhepa mice. We found that NEMOΔhepa/JNKΔhepa livers exhibited overexpression of the interleukin‐6/signal transducer and activator of transcription 3 pathway in addition to epidermal growth factor receptor (EGFR)‐rapidly accelerated fibrosarcoma (Raf)‐mitogen‐activated protein kinase kinase (MEK)‐extracellular signal‐regulated kinase (ERK) cascade. The functional relevance was tested by administering lapatinib, which is a dual tyrosine kinase inhibitor of erythroblastic oncogene B‐2 (ErbB2) and EGFR signaling, to NEMOΔhepa/JNKΔhepa mice. Lapatinib effectively inhibited cystogenesis, improved transaminases, and effectively blocked EGFR‐Raf‐MEK‐ERK signaling. Conclusion : We define a novel function of JNK1/2 in cholangiocyte hyperproliferation. This opens new therapeutic avenues devised to inhibit pathways of cholangiocarcinogenesis.
    Late-spring frost risk between 1959 and 2017 decreased in North America but increased in Europe and Asia
    Zohner, Constantin M. ; Mo, Lidong ; Renner, Susanne S. ; Svenning, Jens Christian ; Vitasse, Yann ; Benito, Blas M. ; Ordonez, Alejandro ; Baumgarten, Frederik ; Bastin, Jean François ; Sebald, Veronica ; Reich, Peter B. ; Liang, Jingjing ; Nabuurs, Gert Jan ; De-Migueln, Sergio ; Alberti, Giorgio ; Antón-Fernández, Clara ; Balazy, Radomir ; Brändli, Urs Beat ; Chen, Han Y.H. ; Chisholm, Chelsea ; Cienciala, Emil ; Dayanandan, Selvadurai ; Fayle, Tom M. ; Frizzera, Lorenzo ; Gianelle, Damiano ; Jagodzinski, Andrzej M. ; Jaroszewicz, Bogdan ; Jucker, Tommaso ; Kepfer-Rojas, Sebastian ; Khan, Mohammed Latif ; Kim, Hyun Seok ; Korjus, Henn ; Johannsen, Vivian Kvist ; Laarmann, Diana ; Langn, Mait ; Zawila-Niedzwiecki, Tomasz ; Niklaus, Pascal A. ; Paquette, Alain ; Pretzsch, Hans ; Saikia, Purabi ; Schall, Peter ; Seben, Vladimír ; Svoboda, Miroslav ; Tikhonova, Elena ; Viana, Helder ; Zhang, Chunyu ; Zhao, Xiuhai ; Crowther, Thomas W. - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)22. - ISSN 0027-8424
    Climate change - Freezing damage - Late frost - Phenology - Spring leaf-out

    Late-spring frosts (LSFs) affect the performance of plants and animals across the world's temperate and boreal zones, but despite their ecological and economic impact on agriculture and forestry, the geographic distribution and evolutionary impact of these frost events are poorly understood. Here, we analyze LSFs between 1959 and 2017 and the resistance strategies of Northern Hemisphere woody species to infer trees' adaptations for minimizing frost damage to their leaves and to forecast forest vulnerability under the ongoing changes in frost frequencies. Trait values on leaf-out and leaf-freezing resistance come from up to 1,500 temperate and boreal woody species cultivated in common gardens. We find that areas in which LSFs are common, such as eastern North America, harbor tree species with cautious (late-leafing) leaf-out strategies. Areas in which LSFs used to be unlikely, such as broad-leaved forests and shrublands in Europe and Asia, instead harbor opportunistic tree species (quickly reacting to warming air temperatures). LSFs in the latter regions are currently increasing, and given species' innate resistance strategies, we estimate that ∼35% of the European and ∼26% of the Asian temperate forest area, but only ∼10% of the North American, will experience increasing late-frost damage in the future. Our findings reveal region-specific changes in the spring-frost risk that can inform decision-making in land management, forestry, agriculture, and insurance policy.

    Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)4. - ISSN 1087-0156 - 1 p.

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    The future of phenomics in dairy cattle breeding
    Cole, John B. ; Eaglen, Sophie A.E. ; Maltecca, Christian ; Mulder, Han A. ; Pryce, Jennie E. - \ 2020
    Animal Frontiers 10 (2020)2. - ISSN 2160-6056 - p. 37 - 44.
    Analytics - Big data - Dairy cattle - Machine learning - Phenomics - Sensors

    Increasingly complex dairy cattle production systems require that all aspects of animal performance are measured across individuals' lifetimes. Selection emphasis is shifting away from traits related to animal productivity toward those related to effcient resource utilization and improved health and welfare/ resilience. The goal of phenomics is to provide information for making decisions related to on-farm management, as well as genetic improvement.

    Future of the human climate niche
    Xu, Chi ; Kohler, Timothy A. ; Lenton, Timothy M. ; Svenning, Jens Christian ; Scheffer, Marten - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Climate - Migration - Societies

    All species have an environmental niche, and despite technological advances, humans are unlikely to be an exception. Here, we demonstrate that for millennia, human populations have resided in the same narrow part of the climatic envelope available on the globe, characterized by a major mode around ~11 °C to 15 °C mean annual temperature (MAT). Supporting the fundamental nature of this temperature niche, current production of crops and livestock is largely limited to the same conditions, and the same optimum has been found for agricultural and nonagricultural economic output of countries through analyses of year-to-year variation. We show that in a business-as-usual climate change scenario, the geographical position of this temperature niche is projected to shift more over the coming 50 y than it has moved since 6000 BP. Populations will not simply track the shifting climate, as adaptation in situ may address some of the challenges, and many other factors affect decisions to migrate. Nevertheless, in the absence of migration, one third of the global population is projected to experience a MAT >29 °C currently found in only 0.8% of the Earth's land surface, mostly concentrated in the Sahara. As the potentially most affected regions are among the poorest in the world, where adaptive capacity is low, enhancing human development in those areas should be a priority alongside climate mitigation.

    Turning autophobic wetting on biomimetic surfaces into complete wetting by wetting additives
    Leermakers, Frans A.M. ; Luengo, Gustavo S. ; Baghdadli, Nawel ; Mazilier, Christian ; Potter, Anne ; Léonforte, Fabien - \ 2020
    Soft Matter 16 (2020)20. - ISSN 1744-683X - p. 4823 - 4839.

    Autophobicity or pseudo partial wetting, a phenomenon of a liquid not spreading on its own monolayer, is characterized by an energy barrier that prevents the growth of a wetting film beyond the monolayer thickness. Applying a molecularly detailed self-consistent field theory we illustrate how autophobic wetting can be overcome by wetting additives. More specifically we use an emulsifier which keeps the interfacial tension between the wetting component and the majority solvent low, and a co-solvent additive which partitions inside the film and then destroys the molecular order in it so that the barrier for film growth is cleared. An application wherein it is believed that autophobic wetting is counteracted by such a set of wetting additives is found in an antidandruff shampoo formulation. We have experimental results that show thick deposits onto hydrophobic hair surfaces by administration of the antidandruff shampoo. The complementary modeling of such a system suggests that the active ingredient plays the role of the co-solvent additive. As significant amounts of the co-solvent additives are needed to approach the completely wet state, the formulation naturally brings large amounts of active ingredient to the root of the hair where its presence is required.

    Antenatal multiple micronutrient supplementation: call to action for change in recommendation
    Bourassa, Megan W. ; Osendarp, Saskia J.M. ; Adu‐Afarwuah, Seth ; Ahmed, Saima ; Ajello, Clayton ; Bergeron, Gilles ; Black, Robert ; Christian, Parul ; Cousens, Simon ; Pee, Saskia de; Dewey, Kathryn G. ; Arifeen, Shams El ; Engle‐Stone, Reina ; Fleet, Alison ; Gernand, Alison D. ; Hoddinott, John ; Klemm, Rolf ; Kraemer, Klaus ; Kupka, Roland ; McLean, Erin ; Moore, Sophie E. ; Neufeld, Lynnette M. ; Persson, L. ; Rasmussen, Kathleen M. ; Shankar, Anuraj H. ; Smith, Emily ; Sudfeld, Christopher R. ; Udomkesmalee, Emorn ; Vosti, Stephen A. - \ 2020
    Annals of the New York Academy Of Sciences 1465 (2020)1. - ISSN 0077-8923 - p. 5 - 7.
    A schematic sampling protocol for contaminant monitoring in raptors
    Espín, Silvia ; Andevski, Jovan ; Duke, Guy ; Eulaers, Igor ; Gómez-Ramírez, Pilar ; Hallgrimsson, Gunnar Thor ; Helander, Björn ; Herzke, Dorte ; Jaspers, Veerle L.B. ; Krone, Oliver ; Lourenço, Rui ; María-Mojica, Pedro ; Martínez-López, Emma ; Mateo, Rafael ; Movalli, Paola ; Sánchez-Virosta, Pablo ; Shore, Richard F. ; Sonne, Christian ; Brink, Nico W. van den; Hattum, Bert van; Vrezec, Al ; Wernham, Chris ; García-Fernández, Antonio J. - \ 2020
    Ambio (2020). - ISSN 0044-7447
    Best practices - Birds of prey - Falcons - Large-scale biomonitoring - Owls - Pan-European network

    Birds of prey, owls and falcons are widely used as sentinel species in raptor biomonitoring programmes. A major current challenge is to facilitate large-scale biomonitoring by coordinating contaminant monitoring activities and by building capacity across countries. This requires sharing, dissemination and adoption of best practices addressed by the Networking Programme Research and Monitoring for and with Raptors in Europe (EURAPMON) and now being advanced by the ongoing international COST Action European Raptor Biomonitoring Facility. The present perspective introduces a schematic sampling protocol for contaminant monitoring in raptors. We provide guidance on sample collection with a view to increasing sampling capacity across countries, ensuring appropriate quality of samples and facilitating harmonization of procedures to maximize the reliability, comparability and interoperability of data. The here presented protocol can be used by professionals and volunteers as a standard guide to ensure harmonised sampling methods for contaminant monitoring in raptors.

    Reproducible molecular networking of untargeted mass spectrometry data using GNPS
    Aron, Allegra T. ; Gentry, Emily C. ; McPhail, Kerry L. ; Nothias, Louis Félix ; Nothias-Esposito, Mélissa ; Bouslimani, Amina ; Petras, Daniel ; Gauglitz, Julia M. ; Sikora, Nicole ; Vargas, Fernando ; Hooft, Justin J.J. van der; Ernst, Madeleine ; Kang, Kyo Bin ; Aceves, Christine M. ; Caraballo-Rodríguez, Andrés Mauricio ; Koester, Irina ; Weldon, Kelly C. ; Bertrand, Samuel ; Roullier, Catherine ; Sun, Kunyang ; Tehan, Richard M. ; Boya P, Cristopher A. ; Christian, Martin H. ; Gutiérrez, Marcelino ; Ulloa, Aldo Moreno ; Tejeda Mora, Javier Andres ; Mojica-Flores, Randy ; Lakey-Beitia, Johant ; Vásquez-Chaves, Victor ; Zhang, Yilue ; Calderón, Angela I. ; Tayler, Nicole ; Keyzers, Robert A. ; Tugizimana, Fidele ; Ndlovu, Nombuso ; Aksenov, Alexander A. ; Jarmusch, Alan K. ; Schmid, Robin ; Truman, Andrew W. ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
    Nature protocols 15 (2020). - ISSN 1754-2189 - p. 1954 - 1991.

    Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking—one of the main analysis tools used within the GNPS platform—creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

    Genomic Breeding Programs Realize Larger Benefits by Cooperation in the Presence of Genotype × Environment Interaction Than Conventional Breeding Programs
    Cao, Lu ; Liu, Huiming ; Mulder, Han A. ; Henryon, Mark ; Thomasen, Jørn Rind ; Kargo, Morten ; Sørensen, Anders Christian - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    across-environment selection of sires - genetic gain - joint genetic evaluation - long-term cooperation - rate of inbreeding - stochastic simulation

    Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment. Two populations had either equal or unequal population sizes. Selection of sires was done either across environments (cooperative) or within their own environment (independent). Four scenarios, (GS/PS) × (cooperative/independent), were performed. The genetic correlation (rg) between the single breeding goal trait expressed in two environments was varied between 0.5 and 0.9. We compared scenarios for genetic gain, rate of inbreeding, proportion of selected external sires, and the split-point rg that is the lowest value of rg for long-term cooperation. Between two equal-sized populations, cooperative GS breeding programs achieved a maximum increase of 19.3% in genetic gain and a maximum reduction of 24.4% in rate of inbreeding compared to independent GS breeding programs. The increase in genetic gain and the reduction in rate of inbreeding realized by GS breeding programs with cooperation were respectively at maximum 9.7% and 24.7% higher than those realized by PS breeding programs with cooperation. Secondly, cooperative GS breeding programs allowed a slightly lower split-point rg than cooperative PS breeding programs (0.85∼0.875 vs ≥ 0.9). Between two unequal-sized populations, cooperative GS breeding programs realized higher increase in genetic gain and showed greater probability for long-term cooperation than cooperative PS breeding programs. Secondly, cooperation using GS were more beneficial to the small population while also beneficial but much less to the large population. In summary, by cooperation in the presence of G × E, GS breeding programs realize larger improvements in terms of the genetic gain and rate of inbreeding, and have greater possibility of long-term cooperation than conventional PS breeding programs. Therefore, we recommend cooperative GS breeding programs in situations with mild to moderate G × E, depending on the sizes of two populations.

    Determinants of legacy effects in pine trees – implications from an irrigation-stop experiment
    Zweifel, Roman ; Etzold, Sophia ; Sterck, Frank ; Gessler, Arthur ; Anfodillo, Tommaso ; Mencuccini, Maurizio ; Arx, Georg von; Lazzarin, Martina ; Haeni, Matthias ; Feichtinger, Linda ; Meusburger, Katrin ; Knuesel, Simon ; Walthert, Lorenz ; Salmon, Yann ; Bose, Arun K. ; Schoenbeck, Leonie ; Hug, Christian ; Girardi, Nicolas De; Giuggiola, Arnaud ; Schaub, Marcus ; Rigling, Andreas - \ 2020
    New Phytologist 227 (2020)4. - ISSN 0028-646X - p. 1081 - 1096.
    cambial activity - drought stress - ecological memory - irrigation experiment - osmoregulation - point dendrometer - radial stem growth - TreeNet

    Tree responses to altered water availability range from immediate (e.g. stomatal regulation) to delayed (e.g. crown size adjustment). The interplay of the different response times and processes, and their effects on long-term whole-tree performance, however, is hardly understood. Here we investigated legacy effects on structures and functions of mature Scots pine in a dry inner-Alpine Swiss valley after stopping an 11-yr lasting irrigation treatment. Measured ecophysiological time series were analysed and interpreted with a system-analytic tree model. We found that the irrigation stop led to a cascade of downregulations of physiological and morphological processes with different response times. Biophysical processes responded within days, whereas needle and shoot lengths, crown transparency, and radial stem growth reached control levels after up to 4 yr only. Modelling suggested that organ and carbon reserve turnover rates play a key role for a tree’s responsiveness to environmental changes. Needle turnover rate was found to be most important to accurately model stem growth dynamics. We conclude that leaf area and its adjustment time to new conditions is the main determinant for radial stem growth of pine trees as the transpiring area needs to be supported by a proportional amount of sapwood, despite the growth-inhibiting environmental conditions.

    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    Combining recent nutritional data with prospective cohorts to quantify the impact of modern dietary patterns on disability–adjusted life years : A feasibility study
    Krieger, Jean Philippe ; Pestoni, Giulia ; Frehner, Anita ; Schader, Christian ; Faeh, David ; Rohrmann, Sabine - \ 2020
    Nutrients 12 (2020)3. - ISSN 2072-6643
    DALYs - Dietary patterns - MenuCH

    Unhealthy diets are commonly associated with increased disability-adjusted life years (DALYs) from noncommunicable diseases. The association between DALYs and dietary patterns can be quantified with individual longitudinal data. This assessment, however, is often based on dietary data collected once at cohort entry, therefore reflecting the impact of “old” dietary habits on morbidity and mortality. To overcome this limitation, we tested the association of contemporary diets with DALYs. First, we defined contemporary dietary patterns consumed in Switzerland with the national nutrition survey menuCH (2014–2015). Second, we identified individuals who consumed similar diets in the NRP–MONICA census-linked cohort (1977–2015). In this cohort, individual data on disease and mortality were used to calculate the DALYs-dietary patterns association using a mixed regression model. A total of 58,771 DALYs from NCDs were recorded in a mean follow-up time of 25.5 years. After multivariable adjustments, the “Swiss traditional” pattern was not associated with an increase in DALYs compared to the “Prudent” pattern. However, individuals following a “Western” pattern had, on average 0.29 DALYs (95% CI 0.02, 0.56) more than those following a “Prudent” pattern, equating to a loss of healthy life of more than three months. These data highlight the feasibility of quantifying the impact of contemporary diets on DALYs without the establishment of new cohorts or the use of nationally aggregated data.

    Scaling carbon fluxes from eddy covariance sites to globe : Synthesis and evaluation of the FLUXCOM approach
    Jung, Martin ; Schwalm, Christopher ; Migliavacca, Mirco ; Walther, Sophia ; Camps-Valls, Gustau ; Koirala, Sujan ; Anthoni, Peter ; Besnard, Simon ; Bodesheim, Paul ; Carvalhais, Nuno ; Chevallier, Frederic ; Gans, Fabian ; Goll, Daniel S. ; Haverd, Vanessa ; Köhler, Philipp ; Ichii, Kazuhito ; Jain, Atul K. ; Liu, Junzhi ; Lombardozzi, Danica ; Nabel, Julia E.M.S. ; Nelson, Jacob A. ; O'Sullivan, Michael ; Pallandt, Martijn ; Papale, Dario ; Peters, Wouter ; Pongratz, Julia ; Rödenbeck, Christian ; Sitch, Stephen ; Tramontana, Gianluca ; Walker, Anthony ; Weber, Ulrich ; Reichstein, Markus - \ 2020
    Biogeosciences 17 (2020)5. - ISSN 1726-4170 - p. 1343 - 1365.

    FLUXNET comprises globally distributed eddy-covariance-based estimates of carbon fluxes between the biosphere and the atmosphere. Since eddy covariance flux towers have a relatively small footprint and are distributed unevenly across the world, upscaling the observations is necessary to obtain global-scale estimates of biosphere-atmosphere exchange. Based on cross-consistency checks with atmospheric inversions, sun-induced fluorescence (SIF) and dynamic global vegetation models (DGVMs), here we provide a systematic assessment of the latest upscaling efforts for gross primary production (GPP) and net ecosystem exchange (NEE) of the FLUXCOM initiative, where different machine learning methods, forcing data sets and sets of predictor variables were employed. Spatial patterns of mean GPP are consistent across FLUXCOM and DGVM ensembles ( at 1 spatial resolution) while the majority of DGVMs show, for 70 of the land surface, values outside the FLUXCOM range. Global mean GPP magnitudes for 2008-2010 from FLUXCOM members vary within 106 and 130 PgC class with the largest uncertainty in the tropics. Seasonal variations in independent SIF estimates agree better with FLUXCOM GPP (mean global pixel-wise) than with GPP from DGVMs (mean global pixel-wise). Seasonal variations in FLUXCOM NEE show good consistency with atmospheric inversion-based net land carbon fluxes, particularly for temperate and boreal regions. Interannual variability of global NEE in FLUXCOM is underestimated compared to inversions and DGVMs. The FLUXCOM version which also uses meteorological inputs shows a strong co-variation in interannual patterns with inversions (for 2001-2010). Mean regional NEE from FLUXCOM shows larger uptake than inversion and DGVM-based estimates, particularly in the tropics with discrepancies of up to several hundred grammes of carbon per square metre per year. These discrepancies can only partly be reconciled by carbon loss pathways that are implicit in inversions but not captured by the flux tower measurements such as carbon emissions from fires and water bodies. We hypothesize that a combination of systematic biases in the underlying eddy covariance data, in particular in tall tropical forests, and a lack of site history effects on NEE in FLUXCOM are likely responsible for the too strong tropical carbon sink estimated by FLUXCOM. Furthermore, as FLUXCOM does not account for fertilization effects, carbon flux trends are not realistic. Overall, current FLUXCOM estimates of mean annual and seasonal cycles of GPP as well as seasonal NEE variations provide useful constraints of global carbon cycling, while interannual variability patterns from FLUXCOM are valuable but require cautious interpretation. Exploring the diversity of Earth observation data and of machine learning concepts along with improved quality and quantity of flux tower measurements will facilitate further improvements of the FLUXCOM approach overall.

    MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)3. - ISSN 1087-0156 - p. 272 - 276.
    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    From GWAS Peak to Causal Mutation; Utilizing p(ig)CADD Scores to Prioritize Sequence Variation
    Derks, Martijn ; Gross, Christian ; Lopes, M.S. ; Reinders, M.J.T. ; Bosse, Mirte ; Gjuvsland, Arne B. ; Megens, Hendrik-Jan ; Ridder, Dick de; Groenen, Martien - \ 2020
    The genotype-phenotype link is a major research topic in life sciences, but remains highly complex to disentangle. Part of the complexity arises from the polygenicity of phenotypes, in which many (interacting) genes contribute to the observed phenotype. Genome wide association studies have been instrumental to associate genomic markers to important phenotypes. However, despite the vast increase of molecular data (e.g. whole genome sequences), pinpointing the causal variant underlying a phenotype of interest is still a major challenge, especially due to high levels of linkage disequilibrium.

    In this study we present a method to prioritize genomic variation underlying traits of interest from genome wide association studies in pigs. First, we select all sequence variants associated with the trait. Subsequently, we prioritize variation by utilizing and integrating predicted variant impact scores, gene expression data, epigenetic marks for promotor and enhancer identification, and associated phenotypes in other (well-studied) mammalian species. The power of the method heavily relies on variant impact scores, for which we used pCADD, a tool which can assign scores to any
    variant in the genome including those in non-coding regions. Using our methodology, we are able to either pinpoint the likely causal mutation or substantially narrow down the list of potential causal candidates from any association result. We demonstrate the efficacy of the tool by reporting known and novel causal variants, of which many affect (non-coding) regulatory sequences associated with important phenotypes in pigs.

    This study provides a framework to pinpoint likely causal variation and genes underlying important phenotypes in pigs. Hence, the tool accelerates the discovery of new causal variants that could be directly implemented to improve selection. Finally, we report several common pathways and molecular mechanisms involved in analogous phenotypes between human and pig, proving the suitability of pig as a model to study human (metabolic) disease.
    Synchronization of developmental, molecular and metabolic aspects of source–sink interactions
    Fernie, Alisdair R. ; Bachem, Christian W.B. ; Helariutta, Yrjö ; Neuhaus, H.E. ; Prat, Salomé ; Ruan, Yong Ling ; Stitt, Mark ; Sweetlove, Lee J. ; Tegeder, Mechthild ; Wahl, Vanessa ; Sonnewald, Sophia ; Sonnewald, Uwe - \ 2020
    Nature Plants 6 (2020). - ISSN 2055-026X - p. 55 - 66.

    Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential. By lifting source and sink activities to their maximum, massive yield increases can be foreseen, potentially closing the future yield gap resulting from an increasing world population and the transition to a carbon-neutral economy. To do so, a better understanding of the interplay between metabolic and developmental processes is required. In the past, these processes have been tackled independently from each other, but coordinated efforts are required to understand the fine mechanics of source–sink relations and thus optimize crop yield. Here, we describe approaches to design high-yielding crop plants utilizing strategies derived from current metabolic concepts and our understanding of the molecular processes determining sink development.

    Soil carbon sequestration in grazing systems: managing expectations
    Godde, Cécile M. ; Boer, Imke J.M. de; Ermgassen, Erasmus zu; Herrero, Mario ; Middelaar, Corina E. van; Muller, Adrian ; Röös, Elin ; Schader, Christian ; Smith, Pete ; Zanten, Hannah H.E. van; Garnett, Tara - \ 2020
    Climatic Change (2020). - ISSN 0165-0009
    Cattle - Climate change - Grasslands - Greenhouse gases - Livestock - Soil carbon

    Grazing systems emit greenhouse gases, which can, under specific agro-ecological conditions, be partly or entirely offset by soil carbon sequestration. However, any sequestration is time-limited, reversible, and at a global level outweighed by emissions from grazing systems. Thus, grazing systems are globally a net contributor to climate change and the time scale of key processes needs to be factored into any mitigation efforts. Failing to do so leads to unrealistic expectations of soil carbon management in grazing systems as a mitigation strategy. Protecting the large carbon stocks in grazing lands is also essential in order to avoid further climate change from additional CO2 release. Despite the time-limited and reversible nature of soil carbon sequestration in grazing lands, sequestration should be promoted in cases where it delivers environmental and agronomic benefits as well as for its potential, particularly on degraded land, to increase the feasibility of limiting global warming to less than 2 or preferably 1.5 °C. Some peer-reviewed sequestration estimates are of a similar order of magnitude to other food systems mitigation options over a 10–20 years period, such as reducing food loss and waste by 15% or aligning diets with current health related dietary-recommendations. However, caution should be applied to such comparisons since mitigation estimates are associated with large uncertainties and will ultimately depend on the economic cost-benefit relation, feasibility of implementation and time frame considered.

    A thin layer of activated carbon deposited on polyurethane cube leads to new conductive bioanode for (plant) microbial fuel cell
    Sudirjo, Emilius ; Constantino Diaz, Paola Y. ; Cociancich, Matteo ; Lisman, Rens ; Snik, Christian ; Buisman, Cees J.N. ; Strik, David P.B.T.B. - \ 2020
    Energies 13 (2020)3. - ISSN 1996-1073
    Activated carbon - Bioanode - Conductive biofilms - Microbial fuel cell - Plant microbial fuel cell - Polyurethane

    Large-scale implementation of (plant) microbial fuel cells is greatly limited by high electrode costs. In this work, the potential of exploiting electrochemically active self-assembled biofilms in fabricating three-dimensional bioelectrodes for (plant) microbial fuel cells with minimum use of electrode materials was studied. Three-dimensional robust bioanodes were successfully developed with inexpensive polyurethane foams (PU) and activated carbon (AC). The PU/AC electrode bases were fabricated via a water-based sorption of AC particles on the surface of the PU cubes. The electrical current was enhanced by growth of bacteria on the PU/AC bioanode while sole current collectors produced minor current. Growth and electrochemical activity of the biofilm were shown with SEM imaging and DNA sequencing of the microbial community. The electric conductivity of the PU/AC electrode enhanced over time during bioanode development. The maximum current and power density of an acetate fed MFC reached 3 mA·m−2 projected surface area of anode compartment and 22 mW·m−3 anode compartment. The field test of the Plant-MFC reached a maximum performance of 0.9 mW·m−2 plant growth area (PGA) at a current density of 5.6 mA·m−2 PGA. A paddy field test showed that the PU/AC electrode was suitable as an anode material in combination with a graphite felt cathode. Finally, this study offers insights on the role of electrochemically active biofilms as natural enhancers of the conductivity of electrodes and as transformers of inert low-cost electrode materials into living electron acceptors.

    PCADD: SNV prioritisation in Sus scrofa
    Groß, Christian ; Derks, Martijn ; Megens, Hendrik Jan ; Bosse, Mirte ; Groenen, Martien A.M. ; Reinders, Marcel ; Ridder, Dick De - \ 2020
    Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X

    Background: In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. Results: To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. Conclusions: We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.

    Model averaging for mapping topsoil organic carbon in France
    Chen, Songchao ; Mulder, Vera Leatitia ; Heuvelink, Gerard B.M. ; Poggio, Laura ; Caubet, Manon ; Román Dobarco, Mercedes ; Walter, Christian ; Arrouays, Dominique - \ 2020
    Geoderma 366 (2020). - ISSN 0016-7061
    Bias-corrected Variance Weighted - Data-poor countries - Digital soil mapping - Sample size requirement - Soil organic carbon

    The soil organic carbon (SOC) pool is the largest terrestrial carbon (C) pool and is two to three times larger than the C stored in vegetation and the atmosphere. SOC is a crucial component within the C cycle, and an accurate baseline of SOC is required, especially for biogeochemical and earth system modelling. This baseline will allow better monitoring of SOC dynamics due to land use change and climate change. However, current estimates of SOC stock and its spatial distribution have large uncertainties. In this study, we test whether we can improve the accuracy of the three existing SOC maps of France obtained at national (IGCS), continental (LUCAS), and global (SoilGrids) scales using statistical model averaging approaches. Soil data from the French Soil Monitoring Network (RMQS) were used to calibrate and evaluate five model averaging approaches, i.e., Granger-Ramanathan, Bias-corrected Variance Weighted (BC-VW), Bayesian Modelling Averaging, Cubist and Residual-based Cubist. Cross-validation showed that with a calibration size larger than 100 observations, the five model averaging approaches performed better than individual SOC maps. The BC-VW approach performed best and is recommended for model averaging. Our results show that 200 calibration observations were an acceptable calibration strategy for model averaging in France, showing that a fairly small number of spatially stratified observations (sampling density of 1 sample per 2500 km2) provides sufficient calibration data. We also tested the use of model averaging in data-poor situations by reproducing national SOC maps using various sized subsets of the IGCS dataset for model calibration. The results show that model averaging always performs better than the national SOC map. However, the Modelling Efficiency dropped substantially when the national SOC map was excluded in model averaging. This indicates the necessity of including a national SOC map for model averaging, even if produced with a small dataset (i.e., 200 samples). This study provides a reference for data-poor countries to improve national SOC maps using existing continental and global SOC maps.

    Politics versus Economics Philosophical Reflections on the Nature of Corporate Governance
    Blok, Vincent - \ 2020
    Philosophy of Management 19 (2020). - ISSN 1740-3812 - p. 69 - 87.
    In this article, we philosophically reflect on the nature of corporate governance. We raise thequestion whether control is still a feasible ideal of corporate governance and reflect on theimplications of the epistemic insufficiency of economic institutions with regard to grandchallenges like of global warming for our conceptualization of corporate governance. We firstintroduce the concept of corporate governance from the perspective of economics and politics.We then trace the genealogy of the concept of governance based on a selective reading ofGiorgio Agamben’s work, who has pointed at two interdependent paradigms of governance inthe Christian tradition, and apply his categories in the context of corporate governance. Wefinally engage in a critical reflection on the concept of corporate governance and develop fourcharacteristics of corporate governance that can guide future conceptual as well as empiricalresearch in the field of corporate social responsibility of economic institutions.
    Efectos de poda y fertilización en los rendimientos de jatropha bajo condiciones de pequeños agricultores en un bosque seco tropical de Ecuador
    Cañadas-López, Álvaro ; Rade-Loor, Diana ; Siegmund-Schultze, Marianna ; Vargas-Hernández, Jesús ; Wehenkel, Christian - \ 2020
    Revista Facultad Nacional de Agronomia Medellin 73 (2020)1. - ISSN 0304-2847 - p. 9089 - 9097.
    Biodiesel - Jatropha curcas - Marginal land - Seed productions

    Jatropha seed is a biomass suitable for bioenergy production that can be produced by smallholders, even on marginal lands. However, the current oilseed production is too low to meet the needs of the planned renewable electricity system in the Galapagos Islands. Pruning and fertilization are management options that can be used to increase the dry seed yields. The effects of both treatments were tested in a split-plot design with jatropha trees, which were monitored during a three-year production period. The average seed production was 643±58 kg ha-1 year-1 in the unpruned trees and 696±50 kg ha-1 year-1 in the pruned trees. Although this difference is small, it is expected to increase over time. The pruned trees developed more slowly than the unpruned trees but showed higher (and still increasing) yields at the end of the three-year test period, while the unpruned trees appeared to have reached their maximum production by the second year of the trial. The low fertilizer doses approved by the smallholders did not have a significant impact on the dry seed yield, and the management options that show benefits in the long term are generally not accepted or adopted by them. Cost-effective nutrient enhancement should be investigated, such as inoculation with arbuscular mycorrhizal fungi.

    International scientists formulate a roadmap for insect conservation and recovery
    Harvey, Jeffrey A. ; Heinen, Robin ; Armbrecht, Inge ; Basset, Yves ; Baxter-Gilbert, James H. ; Bezemer, T.M. ; Böhm, Monika ; Bommarco, Riccardo ; Borges, Paulo A.V. ; Cardoso, Pedro ; Clausnitzer, Viola ; Cornelisse, Tara ; Crone, Elizabeth E. ; Dicke, Marcel ; Dijkstra, Klaas Douwe B. ; Dyer, Lee ; Ellers, Jacintha ; Fartmann, Thomas ; Forister, Mathew L. ; Furlong, Michael J. ; Garcia-Aguayo, Andres ; Gerlach, Justin ; Gols, Rieta ; Goulson, Dave ; Habel, Jan Christian ; Haddad, Nick M. ; Hallmann, Caspar A. ; Henriques, Sérgio ; Herberstein, Marie E. ; Hochkirch, Axel ; Hughes, Alice C. ; Jepsen, Sarina ; Jones, T.H. ; Kaydan, Bora M. ; Kleijn, David ; Klein, Alexandra Maria ; Latty, Tanya ; Leather, Simon R. ; Lewis, Sara M. ; Lister, Bradford C. ; Losey, John E. ; Lowe, Elizabeth C. ; Macadam, Craig R. ; Montoya-Lerma, James ; Nagano, Christopher D. ; Ogan, Sophie ; Orr, Michael C. ; Painting, Christina J. ; Pham, Thai Hong ; Potts, Simon G. ; Rauf, Aunu ; Roslin, Tomas L. ; Samways, Michael J. ; Sanchez-Bayo, Francisco ; Sar, Sim A. ; Schultz, Cheryl B. ; Soares, António O. ; Thancharoen, Anchana ; Tscharntke, Teja ; Tylianakis, Jason M. ; Umbers, Kate D.L. ; Vet, Louise E.M. ; Visser, Marcel E. ; Vujic, Ante ; Wagner, David L. ; Wallis DeVries, Michiel F. ; Westphal, Catrin ; White, Thomas E. ; Wilkins, Vicky L. ; Williams, Paul H. ; Wyckhuys, Kris A.G. ; Zhu, Zeng Rong ; Kroon, Hans de - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 174 - 176.
    Innovatiesubsidie voor medicijnmakers
    Wijffels, Rene ; Adamo, Sarah D'; Barbosa, Maria ; Martens, Dirk ; Südfeld, Christian - \ 2020
    TRY plant trait database – enhanced coverage and open access
    Kattge, Jens ; Bönisch, Gerhard ; Díaz, Sandra ; Lavorel, Sandra ; Prentice, Iain Colin ; Leadley, Paul ; Tautenhahn, Susanne ; Werner, Gijsbert D.A. ; Aakala, Tuomas ; Abedi, Mehdi ; Acosta, Alicia T.R. ; Adamidis, George C. ; Adamson, Kairi ; Aiba, Masahiro ; Albert, Cécile H. ; Alcántara, Julio M. ; Alcázar C, Carolina ; Aleixo, Izabela ; Ali, Hamada ; Amiaud, Bernard ; Ammer, Christian ; Amoroso, Mariano M. ; Anand, Madhur ; Anderson, Carolyn ; Anten, Niels ; Antos, Joseph ; Apgaua, Deborah Mattos Guimarães ; Ashman, Tia Lynn ; Asmara, Degi Harja ; Asner, Gregory P. ; Aspinwall, Michael ; Atkin, Owen ; Aubin, Isabelle ; Baastrup-Spohr, Lars ; Bahalkeh, Khadijeh ; Bahn, Michael ; Bekker, Renee ; Cromsigt, Joris P.G.M. ; Finegan, Bryan ; Kramer, Koen ; Lohbeck, Madelon ; Onoda, Yusuke ; Ozinga, Wim A. ; Prinzing, Andreas ; Robroek, Bjorn ; Slot, Martijn ; Sterck, Frank ; Beest, Mariska te; Bodegom, Peter M. van; Sande, Masha T. van der - \ 2020
    Global Change Biology 26 (2020)1. - ISSN 1354-1013 - p. 119 - 188.
    data coverage - data integration - data representativeness - functional diversity - plant traits - TRY plant trait database

    Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

    Partitioning main carbon pools in a semi-deciduous rainforest in eastern Cameroon
    Zekeng, Jules Christian ; Sande, Masha T. van der; Fobane, Jean Louis ; Mphinyane, Wanda N. ; Sebego, Reuben ; Mbolo, Marguerite Marie Abada - \ 2020
    Forest Ecology and Management 457 (2020). - ISSN 0378-1127
    Biomass - Cameroon - Carbon storage - Climate change - Terra-firme semi-deciduous forest - Tropical rainforest - Variation partitioning

    Tropical forests contribute to climate change mitigation by absorbing carbon from the atmosphere and storing this in biomass and soil organic matter. However, there is still considerable uncertainty about the above- and belowground quantity and distribution of carbon stocks in African forests. Here, we evaluate how different carbon pools (aboveground live biomass, aboveground dead biomass, belowground biomass) contribute to total carbon stocks, and how different carbon components (e.g. large trees, understorey trees, coarse woody debris, roots, soil organic carbon etc.) contribute to carbon pools and total carbon stocks. We evaluated data of extensive inventories within 30 1-ha plots spanning the terra-firme semi-deciduous forest in eastern Cameroon. Hence, the plots were placed at a mean distance of 1 km from the nearest plot and we analyzed the data using variation partitioning, linear regressions and correlation tests. We found that the terra-firme semi-deciduous forests store 283.97 ± 51.42 Mg C ha−1. The aboveground biomass pool, with a carbon stock of 180.99 ± 25.8 Mg C ha−1, mostly explained variation in total carbon stocks (R2 = 0.79). From all aboveground biomass components, carbon in large trees was most strongly correlated with total carbon stocks. The second most important carbon pool was belowground carbon (on average 85.06 ± 16.86 Mg C ha−1; R2 = 0.78), mainly explained by coarse root carbon. Carbon in dead biomass had only a small contribution to total carbon stocks (R2 = 0.04). Hence, our results indicate that aboveground live biomass is a good predictor for variation in total carbon storage within this semi-deciduous terra-firme forest. However, aboveground live carbon and belowground carbon and their interactions explained most of the variation in total carbon stock, indicating that a whole-ecosystem approach is necessary for a full understanding of the carbon cycle.

    Cost and effectiveness of in-season strategies for coping with weather variability in Pakistan's agriculture
    Shah, Hassnain ; Siderius, Christian ; Hellegers, Petra - \ 2020
    Agricultural Systems 178 (2020). - ISSN 0308-521X
    Compounded impacts - Coping - Critical moments - Crop stages - Weather variability

    Crops are vulnerable to weather hazards throughout the growth season, with periods of heightened risk described as critical moments. Farmers have a number of ex-ante and in-season options for coping with these events, and ex-post adjustments to farm-household portfolios to further limit the impact on livelihoods if these options fail. Adaptation-related research has focussed mainly on ex-ante or ex-post coping strategies, because in-season approaches tend to be seen as a given, meaning their cost effectiveness is ignored. Based on detailed survey data collected from 287 households in four of the main cropping systems in Pakistan, this study evaluates the impact pathways of hazards and the cost effectiveness of in-season coping strategies. Yield losses varied by 10–30% for 43% of the cases and by 31–50% for another 39%, with the most severe losses caused by the compounding effect of two hazards in one crop season or if both crops in a multi-crop rotation were affected simultaneously. In-season coping options were mostly restricted to the early crop stages and constrained by a short window of time for the response. The application of in-season coping strategies resulted in a yield recovery of 40–95%, with an additional cost of 4–34% of the value of recovered yield. The major critical moments identified were the harvest season, with farming often affected by un-seasonal precipitation, and the germination stage, with an additional high risk for low temperatures at high altitude. A better understanding of the differentiated risks and effectiveness of in-season coping strategies could support the promotion of sustainable crop production in similar agro-ecologies. Moreover, the effectiveness of present-day coping strategies, rather than the use of coping approaches itself, could signal a potential ability to adjust to future climate change.

    Towards an integrative understanding of soil biodiversity
    Thakur, Madhav P. ; Phillips, Helen R.P. ; Brose, Ulrich ; Vries, Franciska T. De; Lavelle, Patrick ; Loreau, Michel ; Mathieu, Jerome ; Mulder, Christian ; Putten, Wim H. Van der; Rillig, Matthias C. ; Wardle, David A. ; Bach, Elizabeth M. ; Bartz, Marie L.C. ; Bennett, Joanne M. ; Briones, Maria J.I. ; Brown, George ; Decaëns, Thibaud ; Eisenhauer, Nico ; Ferlian, Olga ; Guerra, Carlos António ; König-Ries, Birgitta ; Orgiazzi, Alberto ; Ramirez, Kelly S. ; Russell, David J. ; Rutgers, Michiel ; Wall, Diana H. ; Cameron, Erin K. - \ 2020
    Biological Reviews 95 (2020)2. - ISSN 1464-7931 - p. 350 - 364.
    alpha diversity - beta diversity - biodiversity theory - metacommunity theory - neutral theory - niche theory - spatial scale - species–energy relationship - theory of island biogeography

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

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